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Known bugs in current and previous versions of the Gemini IRAF Package
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Known bugs (and workarounds, where possible) in the Gemini IRAF package
are described here. If you find a new problem, please submit the information via the
Gemini HelpDesk.
- 6 November 2006
- FITCOORDS bug in IRAF 2.13beta2
There is a known bug in IRAF 2.13beta2 FITCOORDS. This will affect users of
the Gemini package who are reducing spectroscopy data. At this time we know
that the problem shows up during the reduction of NIFS data. It is likely
to affect the reduction of the other spectroscopy data at the
fitcoords/transform step.
We recommend that you continue running the Gemini package with IRAF
2.12.2a.
For the Mac Intel users who have to use IRAF 2.13beta2, we suggest you
download and install the unofficial patch below. The fixed code
was graciously provided by the IRAF group. The binaries were compiled at
Gemini. If you encounter problems with it, contact Gemini.
fitcoords213b2-macintel.tar.gz
fitcoords213b2.README
- 20 February 2006
- GNIRS - 2005B and on : two new database files are
needed (Files included in version 1.9 and up)
Due to a change in the GNIRS cameras, two new database files are needed for
reducing 2005B and on GNIRS short camera data with the Gemini/GNIRS IRAF
package (v1.8.1). More information is available in an
email sent to the GNIRS PIs,
and the two files are available below. The updated files will be included
in the next IRAF release.
- 21 September 2005
- Problem with GSFLAT when fl_detec=no and more than
one input flats (version 1.7 and 1.8; fixed in subsequent versions)
When several flats are used as inputs, GSFLAT uses only the first input flat
in the list rather than a combined frame to derive the output flat. This
only happens when fl_detec=no; the fl_detec=yes is not affected by this bug.
The bug affects GSFLAT in Gemini v1.7 and v1.8. Patches have been made
available for both 1.7 and 1.8 versions of the Gemini package:
- 10 November 2004
- nsprepare crashes with bad WCS or fl_checkwcs-
fl_forcewcs+ (version 1.7, fixed in subsequent versions):
The task nsprepare will crash if fl_checkwcs=yes (the default) and the WCS
matrix has a negative determinant. This can be avoided by using
fl_checkwcs=no. However, this then means that fl_forcewcs=yes cannot be
used to correct the WCS. To use fl_forcewcs=yes and fl_checkwcs=yes
together you must zero the values of the CD_ij elements in the PHU (using
hedit) which will allow fl_checkwcs+ to be used without crashing (and so
allow fl_forcewcs to be used too).
Alternatively, you can download this
nsprepare.cl file and replace the
version of it that came with v1.7.
- 4 November 2004
- nireduce crashing when fl_autosky=no (version 1.7,
prior to November 8):
The task nireduce will invariably crash if fl_autosky is set to 'no'. This
problem is caused by a typo that has been introduced in v1.7. Previous versions
are not affected. You can download and install this
patch to remedy the problem
(instructions). If you have
downloaded the v1.7 software from the Gemini web site after November 8, the new
version of nireduce.cl is already included and you do not need to apply the
patch. To verify the version that you are currently running start the CL,
load the gemini package, and type print(gemini.version); if the
version date is '25Oct2004', it is recommended that you install the patch.
- 4 November 2004
- giflat and gifringe having problems with data binned 4
by 4 (version 1.7, prior to November 8):
The tasks giflat and gifringe do not set the default 'statsec' and 'normsec'
correctly for GMOS data binned 4 by 4. You can download and install this
patch to remedy the problem
(instructions). If you have
downloaded the v1.7 software from the Gemini web site after November 8, the new
giflat.cl and gifringe.cl are already included and you do not need to apply the
patch. To verify the version that you are currently running start the CL,
load the gemini package, and type print(gemini.version); if the
version date is '25Oct2004', it is recommended that you install the patch.
- 5 June 2003
- gmosaic and binned images (version 1.4, prior to June 5, 2003,
and version 1.3):
The gmosaic task to mosaicing the GMOS-N detectors does not correctly handle binned images.
The bug affects images that are binned in X as well as images that have different binning
in X and Y. For images binned in X, chip 1 and 3 were placed too far from chip 2 in the
mosaiced image. For images with different binning in X and Y, the rotations of chip 1 and 3
relative to chip 2 was incorrect. Processing of multiple images with binning in X was
also implemented incorrectly. The bugs have been fixed. In addition, the mapping of
chip 3 relative to the other chips has been improved.
If you have installed the Gemini IRAF package v1.4 prior to June 5, 2003,
you can download a new gmosaic.cl file
and replace the old version. You will also need new versions of the bad pixel masks
included with the software:
mgmos_bpm11.pl and
mgmos_bpm22.pl. These files should be copied
to the directory "gmos$data/"
If you have downloaded the software from the Gemini web site after June 5, 2003,
the new versions of gmosaic and the bad pixel masks are included.
Should I rereduce my data? Imaging data with small dither steps show no significant
effect. Unless you are doing high precision astrometry there is no reason to rereduce
imaging data. For spectroscopic data the answer to the question depends on your science.
The effect of the bug on data binned by two in the X-direction is a misplacement
of chip 1 and 3 relative to chip 2 by about two unbinned pixels.
If you are measuring high precision radial velocities
or measuring precise linewidths by fitting template spectra to a large spectral range
you may want to rerun part of the reductions for testing purposes.
However, for measurements of redshifts the effect is too small to cause any significant
effects on the results.
- 5 June 2003
- gnsskysub task missing (version 1.4 only, prior to June 5, 2003):
The task gnsskysub for reduction of Nod-and-Shuffle data from GMOS is missing in the Gemini IRAF package
v1.4. If you have installed the Gemini IRAF package v1.4 prior to June 5, 2003,
you can download the gnsskysub.cl file and
the help page and copy them
to the directories "gmos$" and "gmos$doc/" in your installation.
If you have downloaded the software from the Gemini web site after June 5, 2003, gnsskysub is
included.
- 5 June 2003
- gireduce unstable under Linux/Redhat (version 1.4 prior
to June 5, 2003, and version 1.3):
It has been found that the use of the keypar task to access the image headers is not stable under Linux/Redhat.
gireduce has been updated to use imgets instead. Other tasks affected by this will be updated in
a future release of the Gemini IRAF package.
If you have installed the Gemini IRAF package v1.4 prior to June 5, 2003,
you can download a new gireduce.cl file and replace the old version.
If you have downloaded the software from the Gemini web site after June 5, 2003, the new version
of gireduce is included.
- 8 October 2002
- mkpkg file missing (version v1.4 only, prior to Oct 8, 2002):
The top level mkpkg file was missing in the released version v1.4. If you have downloaded
that version and you need to compile the software, you can download the mkpkg file
here.
If you have downloaded the software from the Gemini web site after Oct 8, 2002, the mkpkg
file was included, and you do not need to download this file separately. The file is
also not needed if you do not need to compile the software. Compilation is not needed
for Solaris/UNIX and Linux operating systems.
- 25 September 2002
- imcoadd (version 1.3 only) - incorrect use of limit parameter:
In the development of the Gemini IRAF package version 1.4 it was found that imcoadd
released with version 1.3 has a bug in the cosmic ray cleaning. The use of the limit
parameter in the case where this is given as a sigma limit above background was
not implemented correctly. Only for the first image in the stack was the implementation
correct. For the remaining images in a stack the limit in counts was set too high.
The result is that the cosmic ray cleaning is done too close to the cores of the
objects. For bright objects and images with differences in the image quality, this
can result in compromised photometry.
The bug is fixed in version 1.4. The bug was not present in releases earlier than v1.3.
- 25 September 2002
- Missing header keywords (version 1.4 and earlier):
The Gemini IRAF package relies on the header keywords for many of the processing steps.
Occasionally, the various tasks will fail to update the headers of intermediate
processing steps correctly. As a result, later steps will fail.
The behaviour is intermittent and has been reported most often under various
versions of Linux.
In some cases, the problem can be solved by re-reducing the images for which the
reduction failed the first time around. In other cases, it has been reported that
manually editing the headers of the intermediate results and then proceeding was
a possible work around.
It is possible that the underlying problem is in the core IRAF. When the Gemini IRAF
package is ported to IRAF 2.12, we will document the problem in more detail and
work with the NOAO/IRAF group to get the problem solved.
- 25 September 2002
- MDFs not found in images (gmos package version 1.4 and earlier):
Occasionally, IRAF will fail attach an MDF to image even though the required
flags are set correctly and the MDF exists. As a result, later steps will fail.
The behaviour is intermittent and has been reported most often under various
versions of Linux.
The problem can be worked around by manually re-attaching the MDF using
the task fitsutil.fxinsert.
It is possible that the underlying problem is in the core IRAF. When the Gemini IRAF
package is ported to IRAF 2.12, we will document the problem in more detail and
work with the NOAO/IRAF group to get the problem solved.
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In original form; Inger Jørgensen
Last update November 6, 2006; Kathleen Labrie